The status of your charges to the agencies will depend upon your contractual relationship with them, the source of the funding and the nature of your business.
If you receive "grants" from the agencies then the payment may not be payment for a supply and may not be subject to VAT. However, from the way in which you describe your relationship with the agencies I think that this is unlikely.
Education that is ultimately funded by the Learning and Skills Council is exempt from VAT.
Education can also be exempt if it is "Private Tuition". Private tuition means the teaching of "a subject ordinarily taught in a school or university". It must be delivered by someone acting independently of an employer, o.e. a sole proprietor or partner in a partnership. If private tuition is given by an employee (or a director of a limited company) then it is taxable.
Outside of the above, education is only exempt if provided by an "eligible body" Eligible bodies include schools, universities, higher education institution, government departments and non-profit making bodies. Unless you fall into one of these categories your supplies will be subject to VAT.
These rules are complex. It may benefit you to seek a full review of your position from a VAT expert. I would be happy to do this for you. I would estimate fees of between £125 and £250 plus VAT.
Regards
Paul Taylor
http://www.vatease.co.uk/
0121 778 4299